From Causal Plausibility to Causal Reliability: Evaluating LLMs as Calibrated Direct Causal-Edge Classifiers

Large language models (LLMs) are increasingly used to provide prior causal knowledge for structural causal discovery, yet whether their direct-edge judgments and confidence can be trusted remains unclear. We systematically evaluate 12 instruction-tuned open-weight models across six benchmark causal graphs, five prompting strategies, and four confidence sources: verbalized, logit-based, cross-prompt agreement, and cross-model agreement. Under our language-only pairwise protocol, our evaluation yields three key findings. (i) LLM-based causal judgments are strongly recall-dominant: models predict overly dense graphs with many false-positive edges, while prompting mainly shifts the precision-recall trade-off rather than resolving overprediction. Gains from model scale diminish on the largest graphs and do not eliminate miscalibration. (ii) LLMs often capture causal relatedness without reliably identifying directness or orientation. Relative to published reference graphs, models misclassify 40.0% of indirect and 36.0% of reversed non-edges as direct edges, versus 28.2% of other non-edges. Moreover, 80.8% and 84.6% of these false positives receive verbalized confidence of at least 80%, revealing substantial overconfidence in structurally incorrect predictions. (iii) Conventional confidence estimates are unreliable, whereas agreement offers a more promising signal. Logit-based confidence frequently collapses near 1.0 regardless of correctness, while cross-prompt and cross-model agreement achieve better mean calibration and discrimination, though their advantages are not statistically significant after Holm correction. A benchmark-familiarity audit further identifies potential familiarity in five model-dataset pairs, all involving AsiaM. Overall, our results suggest LLMs are better viewed as sources of externally validated soft causal priors than as direct evidence of causal structure.

LLM Explainability with Counterfactual Chains and Causal Graphs

Causal graphs provide a high-level language for making mechanisms transparent. Recent work uses Large Language Models (LLMs) to recover causal graphs of external-world processes. Instead, in this paper, we use causal graphs to model LLM inference itself, providing stakeholders with a transparent view of how the model perceives and organizes high-level concepts to produce a prediction. We propose a four-phase method for constructing such graphs. Given a target LLM and a set of textual examples, our method discovers class-discriminative, human-interpretable concepts and maps each input to LLM-perceived concept states. We then introduce an MCMC-inspired counterfactual augmentation procedure that expands the sparse observational data through chains of counterfactuals. This enables stable causal discovery with $σ$-CG, yielding informative, interpretable graphs. We apply our method to three LLMs across disease diagnosis, sentiment analysis, and LLM-as-a-judge classification tasks. We evaluate the learned graphs for predictive fidelity and structural stability, and the MCMC-inspired augmentation for convergence and downstream utility. Our results show that the discovered causal graphs capture meaningful dependencies consistent with LLMs' reasoning. Together, this paper provides a foundation for concept-level explainability of LLMs.